Should I keep things the way they are, label PDF::OCR as deprecated [...]

YES.

Even though we label things as "in development," when we release the code, we have to expect that at some point people will start to regard it as "stable." If you deprecate this module now, these people can continue to use it as long as they want. If you change the API and introduce changes that are incompatible with the old code, you create small management headaches for people that aren't prepared to or are unable to rewrite an application to use the new code base.

Moreover, if someone identifies a serious bug in the old version, how do you fix it for the people that did not upgrade? If someone else offers to maintain the "old" code, how would they be able to fix it? It's not impossible, but at best it will be horribly confusing. More likely it will make people rip their hair out and curse the day you were born.

The harm of changing the namespace is inconsequential compared with the potential harm of not changing it.

You did do the right thing. Anyone that doesn't understand that should receive a full refund of all monies that they paid you for your development efforts on PDF::OCR. They are also welcome to create a branch of PDF::OCR and do things the way they think it should be done. (Maybe they could call their branch PDF::OCR3....)